Anopheles gambiae vs Aedes aegypti (LVP_AGWG) LastZ Results

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Anopheles gambiae (Anopheles gambiae, AgamP4) and Aedes aegypti (LVP_AGWG) (Aedes aegypti, AaegL5) were aligned using the LastZ alignment algorithm (LastZ) in Ensembl Metazoa release . Anopheles gambiae was used as the reference species. After running LastZ, the raw LastZ alignment blocks are chained according to their location in both genomes. During the final netting process, the best sub-chain is chosen in each region on the reference species.

Results

Number of alignment blocks: 63,333

Genome coverage (bp) Coding exon coverage (bp)
Anopheles gambiae

Uncovered: 258,789,954 out of 281,378,673
Covered: 22,588,719 out of 281,378,673

Uncovered: 5,221,254 out of 22,369,942
Matches: 11,737,150 out of 22,369,942
Mismatches: 4,690,596 out of 22,369,942
Insertions: 720,942 out of 22,369,942

Aedes aegypti

Uncovered: 1,255,371,506 out of 1,278,732,104
Covered: 23,360,598 out of 1,278,732,104

Uncovered: 6,539,813 out of 24,304,798
Matches: 12,291,418 out of 24,304,798
Mismatches: 5,128,748 out of 24,304,798
Insertions: 344,819 out of 24,304,798

Configuration parameters

ParameterValue
Gap open penalty (O)400
Gap extend penalty (E)30
HSP threshold (K)
Threshold for gapped extension (L)3000
Threshold for alignments between gapped alignment blocks (H)2200
Masking count (M)
Seed and Transition value (T)1
Scoring matrix (Q)
Default:
     A    C    G    T
    91 -114  -31 -123
  -114  100 -125  -31
   -31 -125  100 -114
  -123  -31 -114   91
Other parameters (other)--ambiguous=iupac

Chunking parameters

Anopheles gambiae Aedes aegypti (LVP_AGWG)
Chunk size 10,000,000 10,100,000
Overlap 0 100,000
Group set size 0 10,100,000
Masking options {default_soft_masking => 1} {default_soft_masking => 1}